bcil/biodocklets repository overview

We present an approach for abstracting the complex data operations of multi-step, bioinformatics pipelines for NGS data analysis. As examples, we have deployed two pipelines for RNAseq and CHIPseq, pre-configured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simple as running a single script This is achieved using a “meta-script” (https://github.com/BCIL/BioDocklets/blob/master/bio-docklets.sh⁠) that automatically starts the Bio-Docklets, and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface (API). The pipeline output is post-processed by integration with the Visual Omics Explorer (VOE, https://academic.oup.com/bioinformatics/article/32/13/2050/1743980/Visual-Omics-Explorer-VOE-a-cross-platform-portal⁠) framework, providing interactive data visualizations that users can access through a web browser.